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Nucleic Acids Research, 2003, Vol. 31, No. 1 51-54
© 2003 Oxford University Press

The UCSC Genome Browser Database

D. Karolchik*, R. Baertsch, M. Diekhans, T. S. Furey, A. Hinrichs, Y. T. Lu, K. M. Roskin, M. Schwartz, C. W. Sugnet, D. J. Thomas, R. J. Weber, D. Haussler and W. J. Kent

Genome Bioinformatics Group, The University of California Santa Cruz (UCSC), School of Engineering, 1156 High Street, Santa Cruz, CA 95064-1077, USA

*To whom correspondence should be addressed. Email: donnak{at}soe.ucsc.edu

ABSTRACT

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.


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 Nucleic Acids ResHome page
L. Bao, M. Zhou, and Y. Cui
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D83 - D87.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
A. Singh, A. Olowoyeye, P. H. Baenziger, J. Dantzer, M. G. Kann, P. Radivojac, R. Heiland, and S. D. Mooney
MutDB: update on development of tools for the biochemical analysis of genetic variation
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D815 - D819.
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 Genome ResHome page
M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, and A. Sandelin
A code for transcription initiation in mammalian genomes
Genome Res., January 1, 2008; 18(1): 1 - 12.
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 GeneticsHome page
G. Abrusan, H.-J. Krambeck, T. Junier, J. Giordano, and P. E. Warburton
Biased Distributions and Decay of Long Interspersed Nuclear Elements in the Chicken Genome
Genetics, January 1, 2008; 178(1): 573 - 581.
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 Hum Mol GenetHome page
A. J. de Smith, A. Tsalenko, N. Sampas, A. Scheffer, N. A. Yamada, P. Tsang, A. Ben-Dor, Z. Yakhini, R. J. Ellis, L. Bruhn, et al.
Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases
Hum. Mol. Genet., December 1, 2007; 16(23): 2783 - 2794.
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 RNAHome page
S. Ro, R. Song, C. Park, H. Zheng, K. M. Sanders, and W. Yan
Cloning and expression profiling of small RNAs expressed in the mouse ovary
RNA, December 1, 2007; 13(12): 2366 - 2380.
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 Toxicol SciHome page
L. J. Martin, H. Chen, X. Liao, H. Allayee, D. M. Shih, G. S. Lee, D. N. Hovland Jr, W. A. Robbins, K. Carnes, R. A. Hess, et al.
FK506, a Calcineurin Inhibitor, Prevents Cadmium-Induced Testicular Toxicity in Mice
Toxicol. Sci., December 1, 2007; 100(2): 474 - 485.
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 Genome ResHome page
J. G. Ruby, A. Stark, W. K. Johnston, M. Kellis, D. P. Bartel, and E. C. Lai
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
Genome Res., December 1, 2007; 17(12): 1850 - 1864.
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 Genome ResHome page
P. P. Luedi, F. S. Dietrich, J. R. Weidman, J. M. Bosko, R. L. Jirtle, and A. J. Hartemink
Computational and experimental identification of novel human imprinted genes
Genome Res., December 1, 2007; 17(12): 1723 - 1730.
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 Mol Biol EvolHome page
M. A. Huntley and A. G. Clark
Evolutionary Analysis of Amino Acid Repeats across the Genomes of 12 Drosophila Species
Mol. Biol. Evol., December 1, 2007; 24(12): 2598 - 2609.
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 Mol Biol EvolHome page
J. Coulombe-Huntington and J. Majewski
Intron Loss and Gain in Drosophila
Mol. Biol. Evol., December 1, 2007; 24(12): 2842 - 2850.
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 Proc. Natl. Acad. Sci. USAHome page
A. Caspi, B. Williams, J. Kim-Cohen, I. W. Craig, B. J. Milne, R. Poulton, L. C. Schalkwyk, A. Taylor, H. Werts, and T. E. Moffitt
Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism
PNAS, November 20, 2007; 104(47): 18860 - 18865.
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 Proc. Natl. Acad. Sci. USAHome page
X. Xiao, Z. Wang, M. Jang, and C. B. Burge
Coevolutionary networks of splicing cis-regulatory elements
PNAS, November 20, 2007; 104(47): 18583 - 18588.
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